COSMIC: High-Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer.

COSMIC (http://cancer.sanger.ac.uk) is an expert-curated database of somatic mutations in human cancer. Broad and comprehensive in scope, recent releases in 2016 describe over 4 million coding mutations across all human cancer disease types. Mutations are annotated across the entire genome, but expert curation is focused on over 400 key cancer genes. Now encompassing the majority of molecular mutation mechanisms in oncogenetics, COSMIC additionally describes 10 million non-coding mutations, 1 million copy-number aberrations, 9 million gene-expression variants, and almost 8 million differentially methylated CpGs. This information combines a consistent interpretation of the data from the major cancer genome consortia and cancer genome literature with exhaustive hand curation of over 22,000 gene-specific literature publications. This unit describes the graphical Web site in detail; alternative protocols overview other ways the entire database can be accessed, analyzed, and downloaded. © 2016 by John Wiley & Sons, Inc.

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.

We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout the human genome, providing an average density on available sequence of one SNP every 1.9 kilobases. These SNPs were primarily discovered by two projects: The SNP Consortium and the analysis of clone overlaps by the International Human Genome Sequencing Consortium. The map integrates all publicly available SNPs with described genes and other genomic features. We estimate that 60,000 SNPs fall within exon (coding and untranslated regions), and 85% of exons are within 5 kb of the nearest SNP. Nucleotide diversity varies greatly across the genome, in a manner broadly consistent with a standard population genetic model of human history. This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.

The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X.

We constructed maps for eight chromosomes (1, 6, 9, 10, 13, 20, X and (previously) 22), representing one-third of the genome, by building landmark maps, isolating bacterial clones and assembling contigs. By this approach, we could establish the long-range organization of the maps early in the project, and all contig extension, gap closure and problem-solving was simplified by containment within local regions. The maps currently represent more than 94% of the euchromatic (gene-containing) regions of these chromosomes in 176 contigs, and contain 96% of the chromosome-specific markers in the human gene map. By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones.

An SNP map of human chromosome 22.

The human genome sequence will provide a reference for measuring DNA sequence variation in human populations. Sequence variants are responsible for the genetic component of individuality, including complex characteristics such as disease susceptibility and drug response. Most sequence variants are single nucleotide polymorphisms (SNPs), where two alternate bases occur at one position. Comparison of any two genomes reveals around 1 SNP per kilobase. A sufficiently dense map of SNPs would allow the detection of sequence variants responsible for particular characteristics on the basis that they are associated with a specific SNP allele. Here we have evaluated large-scale sequencing approaches to obtaining SNPs, and have constructed a map of 2,730 SNPs on human chromosome 22. Most of the SNPs are within 25 kilobases of a transcribed exon, and are valuable for association studies. We have scaled up the process, detecting over 65,000 SNPs in the genome as part of The SNP Consortium programme, which is on target to build a map of 1 SNP every 5 kilobases that is integrated with the human genome sequence and that is freely available in the public domain.

Fine-mapping, genomic organization, and transcript analysis of the human ubiquitin-conjugating enzyme gene UBE2L3.

The human UBE2L3 gene encodes the ubiquitin-conjugating enzyme UbcH7, demonstrated to participate in the ubiquitination of p53, c-Fos, and NF-kappaB in vitro. We report the fine-mapping of this four-exon gene to chromosome 22q11.2. We have constructed a comprehensive genomic clone contig across this gene, demonstrating that the gene lies adjacent to the microsatellite marker D22S446 and spans approximately 57 kb. Four mRNA species are transcribed from this gene, differing in the length of their 3' UTR. Sequence comparison of the UBE2L3 cDNA with its murine homologue reveals a remarkably high degree of sequence conservation within the 3'UTR.

Gelatine colour measurement.

Gelatine colour is of commercial and scientific significance and yet there is no nationally accepted method for its measurement. On analysis it was found that light scatter due to imperfect filtration and molecular size (Veis, 1964) were the sources of interference. Colour measurements using a particular set-up of the BYK-Gardner Color-View Spectrophotometer were found to measure the colour of molten gelatine solutions from the Bloom strength determination, by reflectance, in agreement with visual colour values (r = 0.97), ascribed in accord with Beer's law. Type A and Type B gelatines (67), with turbidities of <80 NTU, from a wide range of raw materials and manufacturers were assessed.

Refined mapping and YAC contig construction of the X-linked cleft palate and ankyloglossia locus (CPX) including the proximal X-Y homology breakpoint within Xq21.3.

The gene for X-linked cleft palate (CPX) has previously been mapped in an Icelandic kindred between the unordered proximal markers DXS1002/DXS349/DXS95 and the distal marker DXYS1X, which maps to the proximal end of the X-Y homology region in Xq21.3. Using six sequence-tagged sites (STSs) within the region, a total of 91 yeast artificial chromosome (YAC) clones were isolated and overlapped in a single contig that spans approximately 3.1 Mb between DXS1002 and DXYS1X. The order of microsatellite and STS markers in this was established as DXS1002-DXS1168-DSX349-DXS95-DXS364-DXS 1196-DXS262-DXS110-DXS1066-(DXS1169, DXS1222)-DXS472-DXS1217-DXYS1X. A long-range restriction map of this region was created using eight nonchimeric, overlapping YAC clones. Analysis of newly positioned polymorphic markers in recombinant individuals from the Icelandic family has enabled us to identify DXS1196 and DXS1217 as the flanking markers for CPX. The maximum physical distance containing the CPX gene has been estimated to be 2.0 Mb, which is spanned by a minimum set of five nonchimeric YAC clones. In addition, YAC end clone and STS analyses have pinpointed the location of the proximal boundary of the X-Y homology region within the map.

A high-density YAC contig map of human chromosome 22.

We have constructed a high-resolution clone map of human chromosome 22 which integrates the available physical and genetic information, establishing a single consensus. The map consists of all classes of DNA landmarks ordered on 705 yeast artificial chromosomes (YACs) at an average landmark density of more than one per 70 kilobases. This map represents the practical limits of currently available YAC resources and provides the basis for determination of the entire gene content and genomic DNA sequence of human chromosome 22.

A YAC contig spanning the ataxia-telangiectasia locus (groups A and C) at 11q22-q23.

Ataxia-telangiectasia (A-T) is an autosomal recessive disease involving cerebellar degeneration, immunodeficiency, cancer predisposition, chromosomal instability and radiosensitivity. A-T is heterogeneous, and the majority of A-T cases are associated with two complementation groups, A and C. The ATA and ATC loci are closely linked at chromosome 11q22-q23. Recombination mapping and linkage disequilibrium analysis have confined both loci between the markers D11S1817 and D11S927, spaced approximately 3.5 Mb apart. Isolation in yeast artificial chromosomes of the genomic segment defined by these loci is essential to identify the gene or genes containing the ATA and ATC mutations. A YAC contig spanning 4.5 Mb, which includes the D11S1817-D11S927 interval, was constructed using two whole genome libraries (ICRF and St. Louis), and a chromosome 11-specific library. Construction of this contig was expedited by prior generation of a region-specific ICRF sublibrary using Alu-PCR products derived from a radiation hybrid. The contig was expanded further by screening the libraries with Alu-PCR products derived from YAC clones and with STSs from YAC ends. YAC clones were aligned by fingerprinting with moderately repetitive probes.

An extended panel of hamster-human hybrids for chromosome 2q.

A hamster-human hybrid containing only the q arm of chromosome 2 has been used to construct a panel of hybrids bearing reduced regions of chromosome 2 using the technique of irradiation fusion gene transfer. The human chromosome 2 carried the Ecogpt gene and all hybrids were selected using this marker. The integrated Ecogpt gene was localized to the region 2q33-34, resulting in the selective retention of this region in the hybrids. These data were combined with another previously constructed panel of hybrids containing regions of 2q, which were enriched for the region 2q36-37. The combined hybrid panel is useful for the mapping of new markers to defined regions of chromosome 2 and for the cloning of genes located on 2q by a positional strategy.

Identification of region-specific yeast artificial chromosomes using pools of Alu element-mediated polymerase chain reaction probes labeled via linear amplification.

The ability to identify large numbers of yeast artificial chromosomes (YACs) specific to any given genomic region rapidly and efficiently enhances both the construction of clone maps and the isolation of region-specific landmarks (e.g., polymorphic markers). We describe a method of preparing region-specific single-stranded hybridization probes from Alu element-mediated polymerase chain reaction (Alu-PCR) products of somatic cell hybrids for YAC library screening. Pools of up to 50 cloned Alu-PCR products from an irradiation-reduced hybrid containing 22q11.2-q13.1 were labeled to high specific activity by linear amplification using a single vector primer. The resulting single-stranded probes were extensively competed to remove repetitive sequences, while retaining the full complexity of the probe. Extensive coverage of the region by YACs using multiple probe pools was demonstrated as many YACs were detected more than once. In situ analysis using chosen YACs confirmed that the clones were specific for the region. Thus, this pooled probe approach constitutes a rapid method to identify large numbers of YACs relevant to a large chromosomal region.

A random STS strategy for construction of YAC contigs spanning defined chromosomal regions.

Sequence tagged sites (STSs) that were generated via Alu-element-mediated polymerase chain reaction (Alu-PCR) and mapped to human Xq26 were used to isolate and overlap yeast artificial chromosomes (YACs). By collating the results of primary pool screening, the order of STSs and YACs was postulated directly. Subsequent isolation of 11 key YACs from 75 positive pools confirmed the proposed contig. Although only a small subset of the available Alu-PCR fragments was used, the STSs were generated at sufficient density to isolate all the YACs required and to identify all except one overlap directly. The results confirmed physical linkage of HPRT to DXS86 and DXS144E. Long-range continuity was determined purely by analysis of the 11 YAC colonies and required no end-rescue. This strategy is therefore an effective approach for the construction of YAC contigs spanning discrete chromosomal regions contained within somatic cell hybrids, with minimal prior knowledge of the region.

Construction of a 2.6-Mb contig in yeast artificial chromosomes spanning the human dystrophin gene using an STS-based approach.

A sequence tagged site (STS)-based approach has been used to construct a 2.6-Mb contig in yeast artificial chromosomes (YACs) spanning the human dystrophin gene. Twenty-seven STSs were used to identify and overlap 34 YAC clones. A DNA fingerprint of each clone produced by direct Alu-PCR amplification of YAC colonies and the isolation of YAC insert ends by vectorette PCR were used to detect overlaps in intron 1 (280 kb) where no DNA sequence data were available, thereby achieving closure of the map. This study has evaluated methods for mapping large regions of the X chromosome and provides a valuable resource of the dystrophin gene in cloned form for detailed analysis of gene structure and function in the future.

Linkage of Emery-Dreifuss muscular dystrophy to the red/green cone pigment (RGCP) genes, proximal to factor VIII.

Further DNA linkage studies on two previously described X-linked recessive Emery-Dreifuss muscular dystrophy (EMD) families are reported, which refine the localization of the gene responsible for EMD. Two recombination events indicate that the most likely localization for the EMD gene lies in the interval between DXS15/DXS52 and F8C. A maximum LOD score of 3.44 at theta = 0 is obtained for EMD vs the red and green cone pigment genes (RCP and GCP). Our data provide additional support for one of the two proposed orientations of genes and markers distal to DXS15/DXS52, with respect to the telomere. Given this favoured orientation, our data best fit a localization of EMD to within a 2 megabase (Mb) interval between DXS15/DXS52 and F8C.

Generation of novel sequence tagged sites (STSs) from discrete chromosomal regions using Alu-PCR.

Human DNA segments from discrete chromosomal regions were generated by utilizing Alu-element-based polymerase chain reaction (Alu-PCR) of an irradiation-fusion hybrid containing approximately 10 to 15 Mb of human DNA. Following cloning into a plasmid vector, a subset of the clones was used to generate sequence tagged sites (STSs) de novo. By means of a panel of hybrids containing portions of the human X chromosome, the STSs were shown to localize to two chromosomal regions, Xq24-Xq26 and Xcen-Xq13, reflecting the presence in the irradiation-fusion hybrid of two human chromosome fragments. These results demonstrate that high densities of STSs can be rapidly and efficiently generated from defined regions of the human genome using Alu-PCR.

Molecular deletions in the Duchenne/Becker muscular dystrophy gene.

To gain further information relating to the frequency, position and size of DNA deletions in the Duchenne/Becker muscular dystrophy (D/BMD) gene region, and to detect any correlation of these deletions with phenotype, a large clinic-based population of DMD and BMD patients has been investigated using 13 cloned intragenic sequences. Our of 263 separate patients studied, 75 showed a deletion of at least one locus (28.5%). These represented 25.6% (55/215) of DMD patients and 41.7% (20/48) of BMD patients, suggesting that the milder phenotype is more often likely to be due to a deletion. The deletions range from 6 kilobases (kb) to greater than 1000 kb in size. The distribution of deletions across the gene region shows at least one region (detected by P20) prone to deletion mutations in both DMD and BMD patients. There is no simple correlation of position or extent of deletions with DMD or BMD, although deletion of a specific region towards the 5' end of the gene may be more often associated with a milder phenotype. Apparently similar deletions can give rise to phenotypes differing significantly in severity, presumably indicating further complexities in the molecular or cellular pathology.